Document: Rediscovering Computational Autopoiesis

5 Experimental Protocol

This paper will describe the results from two separate experiments with SCL. In each case the same experimental protocol was followed. Each experiment consisted of 5 runs of SCL. The initial configuration was identical in all runs, and is illustrated in figure 2. This comprises a single artificially constructed cell-like entity, being a closed membrane of L particles enclosing a single K particle. This is embedded in a toroidal space. The five runs in each experiment differed only in the initial state of the underlying pseudo-random number generator. These five distinct initial states are specified in the files run1.stt through run5.stt in the distributed data file archive (scl-data00.tar.gz).

Figure 2: Initial Configuration.

The two experiments differed only in that experiment 1 implemented just the reactions of the qualitative chemistry described in section 2, whereas experiment 2 incorporated the newly rediscovered chain-based bond inhibition interaction (to be discussed in section 7).

SCL supports a variety of parameters controlling reaction rates, mobility parameters, etc. Apart from the parameter controlling the additional interaction just mentioned, these parameters were held constant across all runs and both experiments. These parameter sets for experiments 1 and 2 are specified in the files exp1.prm and exp2.prm respectively, in the distributed data file archive.

The disintegrationProbability parameter was set at 0.001 in all cases.^{<Note 4>} This is the probability that any given L particle will disintegrate per unit time. The membrane in the initial configuration is composed of 12 L particles. It follows that the expected time to first rupture of the initial membrane is given by:

6 Experiment 1

Rediscovering Computational Autopoiesis

4 The SCL Program

Document: Rediscovering Computational Autopoiesis

mcmullin@eeng.dcu.ie